Reference:
H. Cheng, BH. Kim, and N. Grishin (2008). Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets.
J. Mol. Biol. 377(4): 1265-1278
BH. Kim, H. Cheng, and N. Grishin (2009). HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic Acids Res. 37(Web Server issue):W532-8
Comments and suggestions to: grishin@chop.swmed.edu
Query: T517_A.pdb A
Database: SCOP1.69 less than 40% identity downloaded from ASTRAL
| SCOP Id | Protein | SCOP Superfamily | SCOP Fold | SCOP Class |
|
|---|---|---|---|---|---|
| Intermediate | d1saya1 | L-alanine dehydrogenase | NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | α/β |
| Hit | d1vk4a_ | Hypothetical protein TM0415 | Ribokinase-like | Ribokinase-like | α/β |
Query <-- 0.833 --> IntermediateDALI alignment (Z-score: 4.0 Raw score:377.80) query 1 ----------------------GMEN------KKMNLLLfsgdydkALASLIIANAAREM 32 :::: ::::::: :::::::::::::: d1saya1 1 agrlsvqfgarflerqqggrgvLLGGvpgvkpGKVVILG------gGVVGTEAAKMAVGL 54 query 33 EIEVTIFCAfwGLLLLRdpekasqedkslyeqafssltpreaeelplskmnlggigkkml 92 ::::::::: :::::: d1saya1 55 GAQVQIFDI--NVERLS------------------------------------------- 69 query 93 lemmkeekapklsdlLSGARkkEVKFYAXqlsveimgfkkeelfpevqimDVKEYLKNAL 152 ::::: ::::::: :::::::::: d1saya1 70 -------------ylETLFG-sRVELLYS---------------------NSAEIETAVA 94 query 153 ESDLQLFI---------------------------------------------------- 160 :::::::: d1saya1 95 EADLLIGAvlvpgrrapilvpaslveqmrtgsvivdvavdqggcvetlhptshtqptyev 154 query 161 -------------- 161 d1saya1 155 fgvvhygvpnmpga 168 FAST alignment (Normalized score: 3.98 Raw score:652.10) query 1 GME-------------------------------NKKMNLLLFSGDYDK---ALASLIIA 26 :::::: :::::::: d1saya1 1 ---AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVI---------LGGGVVGTEAA 48 query 27 NAAREMEIEVTIFCAFW-GLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLG 85 :::::::::::::: :::: d1saya1 49 KMAVGLGAQVQIFD---INVER-------------------------------------- 67 query 86 GIGKKMLLEMMKEEKAPKLSDLLS--GARKK----EVKFYAXQLSVEIMGFKKEELFPEV 139 :::: :::::: d1saya1 68 ------------------------LSYLET-LFGSRVELLY------------------- 83 query 140 QIMDVKEYLKNALESDLQLFI--------------------------------------- 160 ::::::::::::::::: d1saya1 84 --SNSAEIETAVAEADLLI--GAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCV 139 query 161 ----------------------------- 161 d1saya1 140 ETLHPTSHTQPTYEVFGVVHYGVPNMPGA 168 TMalign alignment (TM-score: 0.40 Raw score:63.78) query 1 ----------------------GME------NKKMNLLLFSGDYDKALASLIIANAAREM 32 ::: :::::::: ::::::::::::::: d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVKPGKVVILG------GGVVGTEAAKMAVGL 54 query 33 EIEVTIFCAFWGLLLLRDPEKASQEDKSLYEQAFSSLTPREAEELPLSKMNLGGIGKKML 92 ::::::::: :::::: : d1saya1 55 GAQVQIFDI--NVERLS------------------------Y------------------ 70 query 93 LEMMKEEKAPKLSDLLSGARKKEVKFYAXQLSVEIMGFKKEELFPEVQIMDVKEYLKNAL 152 ::::::: ::::::: :::::::::: d1saya1 71 --------------LETLFGS-RVELLYS---------------------NSAEIETAVA 94 query 153 ESDLQLF-I--------------------------------------------------- 160 ::::::: : d1saya1 95 EADLLIGAVLVPGRRAPILVPASLVEQMRTGSVIVDVAVDQGGCVETLHPTSHTQPTYEV 154 query 161 -------------- 161 d1saya1 155 FGVVHYGVPNMPGA 168 HHsearch alignment (Probability: 0.08 E-value:0.01) query 21 ASLIIANAAREMEIEVTIF 39 ::::::::::::::::::: d1saya1 43 VGTEAAKMAVGLGAQVQIF 61
Intermediate <-- 1.087 --> HitDALI alignment (Z-score: 4.9 Raw score:549.20) d1saya1 1 agrlsvqfgarflerqqggrgvllggvpgVKPGKVVILGGG----------------VVG 44 :::::::::::: ::: d1vk4a_ 1 --------------------------ihhHHHHMITFIGHVskdvnvvdgkreiaygGGV 34 d1saya1 45 TEAAKMAVGLGAQVQIFDINVE-RLSYLEtLFGS-RVELLYS------------------ 84 :::::::::::::::::::::: :::::: :::: ::::::: d1vk4a_ 35 VMGAITSSLLGVKTKVITKCTReDVSKFS-FLRDnGVEVVFLksprttsienrytresfl 93 d1saya1 85 -------NSAEiETAVaEADLLIGAVLVpgrRAPI-lVPASLVEQMRtgSVIVD-VAVDQ 135 :::: :::: ::::::::::: :::: :::::::::: ::::: ::::: d1vk4a_ 94 isaadpfTESD-LAFI-EGEAVHINPLW--yGEFPedLIPVLRRKVM--FLSADaQGFVR 147 d1saya1 136 ggcvetlhptshtqptyevfgVVHYGVPN----------------------------MPG 167 :::::::: ::: d1vk4a_ 148 vpeneklvyrdwemkekylkyLDLFKVDSreaetltgtndlrescriirsfgakiilATH 207 d1saya1 168 A----------------------------------------------------------- 168 : d1vk4a_ 208 Asgvivfdgnfyeasfrswslegrtgrgdtctaaflvgfvfkkmsiekatkfaaavtsvk 267 d1saya1 169 ---------------- 169 d1vk4a_ 268 mrhpgplrredleais 283 FAST alignment (Normalized score: 3.56 Raw score:777.40) d1saya1 1 AGRLSVQFGARFLERQQGGRGVLLGGVPGVKP------GKVVILGGG------------- 41 :::::: d1vk4a_ 1 --------------------------------IHHHHHHMITFI---GHVSKDVNVVDGK 25 d1saya1 42 ------VVGTEAAKMAVGLGAQVQIFD-INVERLSYLETL-FGSRVELLY---------- 83 ::::::::::::::::::::: :::::::: ::: :::::::: d1vk4a_ 26 REIAYGGGVVMGAITSSLLGVKTKVITKCTREDVSK-FSFLRDNGVEVV-FLKSPRTTSI 83 d1saya1 84 ----------------SNSAEIETAVAE--ADLLIGAVLVPGRR-APILV----PASLVE 120 :::: :::: :::::::: ::::: :::::: d1vk4a_ 84 ENRYTRESFLISAADPFTES-DLAF---IEGEAVHINP------LWYGEFPEDLIPVLRR 133 d1saya1 121 QMRTG-SVIVDVAVDQGGCVETLHPTSHTQPTYEVFG----------------------- 156 : ::::: d1vk4a_ 134 K----VMFLSA--------------------------DAQGFVRVPENEKLVYRDWEMKE 163 d1saya1 157 ------VVHYGVPNMPGA------------------------------------------ 168 :::: d1vk4a_ 164 KYLKYLDLFK--------VDSREAETLTGTNDLRESCRIIRSFGAKIILATHASGVIVFD 215 d1saya1 169 ------------------------------------------------------------ 169 d1vk4a_ 216 GNFYEASFRSWSLEGRTGRGDTCTAAFLVGFVFKKMSIEKATKFAAAVTSVKMRHPGPLR 275 d1saya1 169 -------- 169 d1vk4a_ 276 REDLEAIS 283 TMalign alignment (TM-score: 0.43 Raw score:72.43) d1saya1 1 -----------------A-----------GRLS-VQFGARFLERQQGGRGVLLGGVPGVK 31 : :::: :::::::::: ::: d1vk4a_ 1 IHHHHHHMITFIGHVSKDVNVVDGKREIAYGGGVVMGAITSSLL-----GVK-------- 47 d1saya1 32 PGKVVILGGG--VVGTEAAKMAVGLGAQVQIFDINVERL-----------------SYLE 72 ::::: ::: ::::::::::::::::::: : ::: d1vk4a_ 48 -TKVIT-KCTRE--DVSKFSFLRDNGVEVVFLK-S-PRTTSIENRYTRESFLISAA---- 97 d1saya1 73 TLFGSRVELLYSNSAEIETAVAEA-DLLIGAVLVPGRRA--PILVPASLVEQMRTGSVIV 129 :::::: ::::: :: :::::::: :: :::::::::::::: :::: d1vk4a_ 98 ---------DPFTES-DLAFI-EGEAVHINPLW----YGEFPEDLIPVLRRKVMF-LSAD 141 d1saya1 130 DVAVDQG----------G-----CVE--T--LHP-------------------------- 144 ::::::: : :: : ::: d1vk4a_ 142 AQGFVRVPENEKLVYRDWEMKEK-YLKYLDLFKVDSREAETLTGTNDLRESCRIIRSFGA 200 d1saya1 145 ----TS---HTQ-------------------------PT--YE--VFGV-------V--- 158 :: ::: :: :: ::: : d1vk4a_ 201 KIILATHASGVIVFDGNFYEASFRSWSLEGRTGRGDTCTAAFLVG-FVFKKMSIEKATKF 259 d1saya1 159 HY---GV------PNMPGA----------- 168 : : :: d1vk4a_ 260 -AAAV-TSVKMRH----PGPLRREDLEAIS 283 HHsearch alignment (Probability: 0.06 E-value:0.03) d1saya1 41 GVVGTEAAKMAVGLGAQVQIFDI 63 ::::::::::::::::::::::: d1vk4a_ 31 GGGVVMGAITSSLLGVKTKVITK 53